I have a brand new 2017 3.6 Ecoboost Lariat. When I hook my iPhone 6 (which is fully updated on all apps) via usb it does connect however it won't stay connected. Also when I hook up my iPod it does that same thing will connect but won't stay connected. I have tried multiple cords and both USB ports. Seems it could be a Sync 3 problem?

 

I've had it not connect a few time when first plugged in but always stays connected after a re-plug. I'm using Android so I don't know if that makes a difference.

 

I'm running the public beta for 10.3 seems fine for me

 

Try cleaning out the lightning port. That little guy picks up a lot of lint and dirt. To clean, dig around in there with a toothpick, especially on the rounded ends. Or try some compressed air.